Busquets limped off in the second half of his team's 3-0 victory, which ensured that they would progress to the quarter-finals of the competition courtesy of a 4-1 success.
The Spain international is now facing "approximately three weeks" on the sidelines, which makes him a doubt for the first leg of the Champions League last-eight tie, which will take place on either April 3 or April 4.
"Tests have confirmed that Sergio Busquets has a hairline fracture on the fifth toe of his right foot. He will be out for approximately three weeks," read a statement from Barcelona.
Busquets will also miss Spain's upcoming international friendlies against Germany and Argentina.